FMO DATABASE

FMODB ID: 989N2

Calculation Name: 3E7U-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E7U

Chain ID: X

ChEMBL ID:

UniProt ID: Q53I06

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	37
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-167853.390719
FMO2-HF: Nuclear repulsion	150679.435084
FMO2-HF: Total energy	-17173.955635
FMO2-MP2: Total energy	-17218.019682

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(X:1:GLY)

Summations of interaction energy for fragment #1(X:1:GLY)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-23.743	-16.381	7.809	-7.358	-7.811	-0.039

Interaction energy analysis for fragmet #1(X:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.015

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	X	3	GLY	0	0.071	0.041	3.562	0.537	1.638	0.005	-0.533	-0.572	0.001
4	X	4	CYS	0	-0.084	0.010	2.497	1.505	2.467	0.211	-0.403	-0.771	0.001
5	X	5	ASN	0	0.007	-0.029	2.041	-12.027	-10.691	6.092	-3.975	-3.452	-0.050
6	X	6	GLY	0	0.032	0.017	4.425	0.903	0.973	-0.001	-0.014	-0.055	0.000
7	X	7	PRO	0	-0.028	-0.022	7.285	0.023	0.023	0.000	0.000	0.000	0.000
8	X	8	TRP	0	-0.073	-0.038	10.164	0.163	0.163	0.000	0.000	0.000	0.000
9	X	9	ASP	-1	-0.881	-0.920	7.446	-1.623	-1.623	0.000	0.000	0.000	0.000
10	X	10	GLU	-1	-0.866	-0.934	6.937	-1.729	-1.729	0.000	0.000	0.000	0.000
11	X	11	ASP	-1	-0.774	-0.881	7.602	-0.620	-0.620	0.000	0.000	0.000	0.000
12	X	12	ASP	-1	-0.788	-0.921	8.249	-0.686	-0.686	0.000	0.000	0.000	0.000
13	X	13	MET	0	-0.058	-0.013	9.794	0.216	0.216	0.000	0.000	0.000	0.000
14	X	14	GLN	0	-0.045	-0.025	6.996	-0.021	-0.021	0.000	0.000	0.000	0.000
15	X	15	CYS	0	0.023	0.041	2.825	-5.165	-3.466	0.300	-0.932	-1.067	0.013
16	X	16	HIS	0	0.010	0.004	7.944	0.449	0.449	0.000	0.000	0.000	0.000
17	X	17	ASN	0	-0.064	-0.055	11.602	0.185	0.185	0.000	0.000	0.000	0.000
18	X	18	HIS	0	0.042	0.028	7.469	-0.176	-0.176	0.000	0.000	0.000	0.000
19	X	19	CYS	0	0.007	0.014	8.301	-0.124	-0.124	0.000	0.000	0.000	0.000
20	X	20	LYS	1	0.810	0.903	11.593	-0.072	-0.072	0.000	0.000	0.000	0.000
21	X	21	SER	0	-0.065	-0.026	12.614	0.001	0.001	0.000	0.000	0.000	0.000
22	X	22	ILE	0	-0.011	0.005	10.749	0.017	0.017	0.000	0.000	0.000	0.000
23	X	23	LYS	1	0.962	0.962	15.307	-0.215	-0.215	0.000	0.000	0.000	0.000
24	X	24	GLY	0	0.015	0.006	18.920	0.018	0.018	0.000	0.000	0.000	0.000
25	X	25	TYR	0	-0.039	-0.002	12.530	-0.026	-0.026	0.000	0.000	0.000	0.000
26	X	26	LYS	1	0.926	0.956	16.722	-0.121	-0.121	0.000	0.000	0.000	0.000
27	X	27	GLY	0	0.035	0.001	14.872	-0.061	-0.061	0.000	0.000	0.000	0.000
28	X	28	GLY	0	0.014	-0.002	10.583	0.144	0.144	0.000	0.000	0.000	0.000
29	X	29	TYR	0	0.015	0.024	9.682	-0.042	-0.042	0.000	0.000	0.000	0.000
30	X	31	ALA	0	0.001	-0.011	6.172	0.181	0.181	0.000	0.000	0.000	0.000
31	X	32	LYS	1	0.891	0.929	6.553	-0.530	-0.530	0.000	0.000	0.000	0.000
32	X	33	GLY	0	0.047	0.024	8.205	-0.101	-0.101	0.000	0.000	0.000	0.000
33	X	34	GLY	0	0.104	0.052	6.593	-0.022	-0.022	0.000	0.000	0.000	0.000
34	X	35	PHE	0	-0.042	-0.005	4.014	-1.060	-0.956	0.000	-0.038	-0.065	0.000
35	X	36	VAL	0	-0.036	-0.019	2.706	-3.835	-1.835	1.203	-1.448	-1.755	-0.004
36	X	38	LYS	1	0.873	0.932	4.675	0.203	0.293	-0.001	-0.015	-0.074	0.000
37	X	40	TYR	0	-0.004	-0.002	11.154	-0.032	-0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:1:GLY)